Chemically modified, "functionalized," solid surfaces are necessary in many laboratory procedures involved in chemistry and biotechnology. One important application is in solid phase chemical synthesis, wherein initial derivatization of a substrate surface enables synthesis of polymers such as oligonucleotides and peptides on the substrate itself. Support-bound oligomer arrays, particularly oligonucleotide arrays, may be used in screening studies for determination of binding affinity and in diagnostic applications, i.e., to detect the presence of a nucleic acid containing a specific, known oligonucleotide sequence. Modification of surfaces for use in chemical synthesis has been described, for example, in U.S. Pat. No. 5,624,711 to Sundberg et al., in U.S. Pat. No. 5,266,222 to Willis et al., in U.S. Pat. No. 5,137,765 to Farnsworth, and in numerous other patents and publications.
In modifying siliceous or metal oxide surfaces, one technique that has been used is derivatization with bifunctional silanes, i.e., silanes having a first functional group enabling covalent binding to the surface (often an Si-halogen or Si-alkoxy group, as in --SiCl.sub.3 or --Si(OCH.sub.3).sub.3, respectively) and a second functional group that can impart the desired chemical and/or physical modifications to the surface. A problem with this type of surface modification, however, is that incorporation of a desirable surface chemical functionality--provided by the second functional group--may result in a surface with undesirable physical properties. For example, there is currently a great deal of interest in synthesizing arrays of different oligonucleotides on siliceous surfaces, and a high density of array features is generally considered desirable. The various array features can be independently created by the planar separation of individual phosphoramidite coupling reactions as the oligonucleotides are synthesized; a simple way to achieve this separation is by spotting the phosphoramidite solutions onto the surface. Feature density is then determined by the spread of the solution droplet, which is in turn uniquely determined by both the volume of the droplet and the contact angle between the droplet and the surface. However, to covalently couple the first nucleotide phosphoramidite to the substrate surface requires hydroxyl moieties on the surface, which makes the surface wettable by the phosphoramidite solutions and thus creates droplet spread; for a given droplet volume, then, relatively large array features are provided, limiting feature density.
The aforementioned problem can be overcome using a variety of techniques to constrain the droplets as they are applied to the substrate surface. Permanent wells can be formed by micromachining the substrate, with the active surfaces subsequently modified, constraining the droplet by capillary action. Temporary wells can also be formed using either a pre-formed "stencil" or by applying a coating to the substrate and patterning the coating. These wells could constrain the droplet by either capillary action and/or by using a relatively unwettable coating. Alternatively, as described in U.S. Pat. No. 5,474,796 to Brennan, a pattern of two different surface-bound silanes can be formed by physically masking the surface, depositing the first silane, and then removing the mask and depositing the second silane. This procedure can be used to constrain a droplet by surrounding a reactive spot on the surface, formed by one of the two silanes, with a lower surface energy spot, formed by the other of the two silanes.
All of these procedures, however, require considerable processing and thus add substantially to the time and cost required to fabricate an array. Also, the existence of a pattern on the substrate requires that the array writing apparatus be aligned with the surface pattern, a non-trivial issue for small array features.
The present invention is directed to the aforementioned need in the art, and provides a way of functionalizing substrate surfaces to reduce surface energy and thus constrain droplets of liquid that are applied to the substrate surface, while avoiding the aforementioned problems and difficulties associated with the procedures of the prior art.